Package gorsat.process

Class ProcessIteratorAdaptor

java.lang.Object
org.gorpipe.gor.model.GenomicIterator
org.gorpipe.model.gor.iterators.RowSource
gorsat.process.ProcessIteratorAdaptor
All Implemented Interfaces:
java.lang.AutoCloseable, java.util.Iterator<org.gorpipe.gor.model.Row>
public class ProcessIteratorAdaptor
extends org.gorpipe.model.gor.iterators.RowSource
Created by sigmar on 03/11/15.

  • Nested Class Summary

    Nested classes/interfaces inherited from class org.gorpipe.gor.model.GenomicIterator

    org.gorpipe.gor.model.GenomicIterator.ChromoLookup

  • Constructor Summary

    Constructors 
    Constructor Description
    ProcessIteratorAdaptor​(org.gorpipe.gor.session.GorContext context, java.lang.String cmd, java.lang.String alias, org.gorpipe.model.gor.iterators.RowSource rs, gorsat.Commands.Analysis an, java.lang.String header, boolean skipheader, java.util.Optional<java.lang.String> skip, boolean allowerror, boolean nor)  

  • Method Summary

    Modifier and Type Method Description
    void close()  
    boolean hasNext()  
    boolean isBuffered()  
    org.gorpipe.gor.model.Row next()  
    void setPosition​(java.lang.String seekChr, int seekPos)  
    static void subCommandSplit​(java.nio.file.Path fileRoot, java.lang.String subCommand, java.util.List<java.lang.String> split)  

    Methods inherited from class org.gorpipe.model.gor.iterators.RowSource

    bufferSize, bufferSize_$eq, clone, getAvgBasesPerMilliSecond, getAvgBatchSize, getAvgRowsPerMilliSecond, getAvgSeekTimeMilliSecond, getBufferSize, getCurrentBatchLoc, getCurrentBatchRow, getCurrentBatchSize, getEx, getGorHeader, getParent, moveToPosition, moveToPosition$default$3, next, parent, parent_$eq, seek, setBufferSize, setEx, setParent, terminateReading

    Methods inherited from class org.gorpipe.gor.model.GenomicIterator

    decStat, filter, getColnum, getContext, getHeader, getLookup, getMonitor, getSourceName, incStat, init, initStats, isSourceAlreadyInserted, pushdownCalc, pushdownFilter, pushdownGor, pushdownSelect, pushdownTop, pushdownWrite, seek, select, selectHeader, setColnum, setContext, setHeader, setSourceAlreadyInserted, setSourceName

    Methods inherited from class java.lang.Object

    equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface java.util.Iterator

    forEachRemaining, remove

  • Constructor Details

    • ProcessIteratorAdaptor

      public ProcessIteratorAdaptor​(org.gorpipe.gor.session.GorContext context, java.lang.String cmd, java.lang.String alias, org.gorpipe.model.gor.iterators.RowSource rs, gorsat.Commands.Analysis an, java.lang.String header, boolean skipheader, java.util.Optional<java.lang.String> skip, boolean allowerror, boolean nor) throws java.io.IOException
      Throws:
      java.io.IOException

  • Method Details

    • hasNext

      public boolean hasNext()
      Specified by:
      hasNext in interface java.util.Iterator<org.gorpipe.gor.model.Row>
      Overrides:
      hasNext in class org.gorpipe.gor.model.GenomicIterator

    • next

      public org.gorpipe.gor.model.Row next()
      Specified by:
      next in interface java.util.Iterator<org.gorpipe.gor.model.Row>
      Overrides:
      next in class org.gorpipe.gor.model.GenomicIterator

    • setPosition

      public void setPosition​(java.lang.String seekChr, int seekPos)
      Overrides:
      setPosition in class org.gorpipe.model.gor.iterators.RowSource

    • close

      public void close()
      Specified by:
      close in interface java.lang.AutoCloseable
      Specified by:
      close in class org.gorpipe.model.gor.iterators.RowSource

    • isBuffered

      public boolean isBuffered()
      Overrides:
      isBuffered in class org.gorpipe.model.gor.iterators.RowSource

    • subCommandSplit

      public static void subCommandSplit​(java.nio.file.Path fileRoot, java.lang.String subCommand, java.util.List<java.lang.String> split)